RetrogeneDB - Retrocopy retro_rnor

						
>retro_rnor_1362
CTACATTCAGCAACCTACCAGATTGCCTATCTCCACAGCCGTGGGCCTACTCCCACCGGGCTGCACTGTGTCTGCTGCCC

TGGTTGGAAGAGGACCAGTGGACTCAGTAGGGCTTGTGGAACAGCAACCTGCCAGCCCCAGTGTGGAAAGCGAGGGAGTT

CATTCCATTCAGACCACCACTGCCCTGTGTGATGGTGGGGAGATGCTTGCCAGACGGATGTACATGAAAGCAGTTCTGGA

GAGGCCAGTTGTCCTCCCCGCTATGTCAAAACTGTGGGCAACCAGTGGTTGTGGGTGTTGGGAGGGGTGAAGCCCATCTA

CAGATGGGATGCTCTGCCTACCCAGGGGAGGCCCCTCCCTGGTGACCCCCAAGCCCCACAACTGGAGTGGGCAGCGTGGT

GAGGGAGGAGGTGCATAGTCTGCAGTCCTGGGTTGACATGCTAGAGCAGAAACTGCAGTTGGTGCTGGTCCCTCTG

ORF - retro_rnor_1362 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	61.49 %
Parental protein coverage:	56.99 %
Number of stop codons detected:	2
Number of frameshifts detected	2

Retrocopy - Parental Gene Alignment:

									ParentalIYRTAYRIAYRHSPGLTPSRPRYACCPGWKRTNGLPGACGAAICQPPCGNEGSCIRPGRCRCPVGWQGDT
		.....Y.IAY.HS.G.TP......CCPGWKRT.GL..ACG.A.CQP.CG..GS........CPV.W.GD.
RetrocopyLHSATYQIAYLHSRGPTPTGLHCVCCPGWKRTSGLSRACGTATCQPQCGKRGSSFHSDH-HCPV*WWGDA
ParentalCQIDVDECSTGEARCPQRCVNTVGSYW-CQCWEGQSPSADGVLCLPKEGPSPVA-PSPTPGVDSVVREEV
		CQ.DV.E.S.GEA.CP.R.V.TVG..W.C.CWEG.SPS.DG.LCLP..GPS.V..PSPT.GV.SVVREEV
RetrocopyCQTDVHESSSGEASCPPRYVKTVGNQW>CGCWEG*SPSTDGMLCLPRGGPSLVT>PSPTTGVGSVVREEV
ParentalYKLQARVDVLEQKLQLVLAPL
		..LQ..VD.LEQKLQLVL.PL
RetrocopyHSLQSWVDMLEQKLQLVLVPL

							

							Legend:
							
								*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide

						

RNA-Seq - click to see more details

(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP017611_brain	0 .00 RPM	13 .95 RPM
SRP017611_kidney	0 .00 RPM	24 .07 RPM
SRP017611_liver	0 .07 RPM	10 .56 RPM

ChIP-Seq - click to see more details

Rattus norvegicus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_rnor_1362 retrocopy.

TSS - click to see more details

Rattus norvegicus was not studied using FANTOM5 data.

Lab - click to see more details

retro_rnor_1362 was not experimentally validated.

Retrocopy orthology:

Retrocopy retro_rnor_1362 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Mus musculus	retro_mmus_1736

Parental genes homology:

Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003952	1 retrocopy	retro_amel_1056,
Canis familiaris	ENSCAFG00000019575	1 retrocopy	retro_cfam_945,
Mustela putorius furo	ENSMPUG00000011294	1 retrocopy	retro_mputfur_329,
Mus musculus	ENSMUSG00000026921	1 retrocopy	retro_mmus_1736,
Rattus norvegicus	ENSRNOG00000019388	1 retrocopy	retro_rnor_1362 ,

	RetrogeneDB ID:	retro_rnor_1362
Retrocopy location	Organism:	*Rat (Rattus norvegicus)*
	Coordinates:	18:68844692..68845168(+)
	Located in intron of:	None
Retrocopy information	Ensembl ID:	None
	Aliases:	None
	Status:	NOVEL
Parental gene information	Parental gene summary:
	Parental gene symbol:	Egfl7
	Ensembl ID:	ENSRNOG00000019388
	Aliases:	None
	Description:	EGF-like domain 7 [Source:MGI Symbol;Acc:MGI:2449923]

Parental	IYRTAYRIAYRHSPGLTPSRPRYACCPGWKRTNGLPGACGAAICQPPCGNEGSCIRPGRCRCPVGWQGDT
	.....Y.IAY.HS.G.TP......CCPGWKRT.GL..ACG.A.CQP.CG..GS........CPV.W.GD.
Retrocopy	LHSATYQIAYLHSRGPTPTGLHCVCCPGWKRTSGLSRACGTATCQPQCGKRGSSFHSDH-HCPV*WWGDA

Parental	CQIDVDECSTGEARCPQRCVNTVGSYW-CQCWEGQSPSADGVLCLPKEGPSPVA-PSPTPGVDSVVREEV
	CQ.DV.E.S.GEA.CP.R.V.TVG..W.C.CWEG.SPS.DG.LCLP..GPS.V..PSPT.GV.SVVREEV
Retrocopy	CQTDVHESSSGEASCPPRYVKTVGNQW>CGCWEG*SPSTDGMLCLPRGGPSLVT>PSPTTGVGSVVREEV

Parental	YKLQARVDVLEQKLQLVLAPL
	..LQ..VD.LEQKLQLVL.PL
Retrocopy	HSLQSWVDMLEQKLQLVLVPL

*	Stop codon
>	Forward frameshift by one nucleotide
<	Reverse frameshift by one nucleotide

RetrogeneDB ID:

retro_rnor_1362